Single-cell analysis in Python. Scales to >100M cells.

Annotated data.

muon is a multimodal omics Python framework

Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.

Multimodal Data (.h5mu) implementation for Python

Unsupervised Deep Disentangled Representation of Single-Cell Omics

Feature-rich Python implementation of the tximport package for gene count estimation.

pseudobulking on an AnnData object

The AnnSQL package enables SQL based queries on AnnData objects.

Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData

A user-friendly library that brings familiar DataFrame-style operations to AnnData objects with a simple and expressive API.

anndata with trees

Agentic Cell type annotation for Anndata objects

Multimodal datasets, in MuData format

Seurat to AnnData conversion

Lift annotations from a GTF file to an adata object.

AnnData-compatible wrapper of Spotify's annoy library.

Neighbor graphs for single-cell data (AnnData)